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- PDB-5mul: Glycoside Hydrolase BT3686 bound to Glucuronic Acid -

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Basic information

Entry
Database: PDB / ID: 5mul
TitleGlycoside Hydrolase BT3686 bound to Glucuronic Acid
ComponentsNeuraminidase
KeywordsHYDROLASE / Rhamnosidase / Bacteroides / Beta-propeller / hydrolase
Function / homologySialidase superfamily / BNR repeat-containing family member / BNR repeat-containing family member / Neuraminidase
Function and homology information
Specimen sourceBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.39 Å resolution
AuthorsMunoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Henrissat, B. / Gilbert, H.J.
Funding supportUnited Kingdom , 1 items
OrganizationGrant numberCountry
European Research Council322820United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unusual active site location and catalytic apparatus in a glycoside hydrolase family.
Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Henrissat, B. / Gilbert, H.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 13, 2017 / Release: Apr 26, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 26, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7152
Polyers49,5211
Non-polymers1941
Water5,008278
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)380
ΔGint (kcal/M)3
Surface area (Å2)15520
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)120.178, 120.178, 52.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP 61

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Components

#1: Protein/peptide Neuraminidase /


Mass: 49521.020 Da / Num. of mol.: 1
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_3686 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1H5
#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 / Density percent sol: 44.5 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 200 mM Potassium Acetate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.01 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Collection date: Feb 5, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionD resolution high: 1.39 Å / D resolution low: 21.75 Å / Number obs: 436522 / NetI over sigmaI: 13.5 / Redundancy: 5 % / Percent possible obs: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Correlation coeff Fo to Fc: 0.971 / Correlation coeff Fo to Fc free: 0.966 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 0.894 / Overall SU ML: 0.036 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.055 / Overall ESU R Free: 0.057
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso mean: 19.22 Å2 / Aniso B11: -0.18 Å2 / Aniso B12: -0.09 Å2 / Aniso B13: - Å2 / Aniso B22: -0.18 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.6 Å2
Least-squares processR factor R free: 0.19423 / R factor R work: 0.17293 / R factor obs: 0.17397 / Highest resolution: 1.39 Å / Lowest resolution: 21.75 Å / Number reflection R free: 4366 / Number reflection obs: 82358 / Percent reflection R free: 5 / Percent reflection obs: 99.56
Refine hist #1Highest resolution: 1.39 Å / Lowest resolution: 21.75 Å
Number of atoms included #1Protein: 3012 / Nucleic acid: 0 / Ligand: 13 / Solvent: 278 / Total: 3303
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193303
X-RAY DIFFRACTIONr_bond_other_d0.0020.0202910
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9294531
X-RAY DIFFRACTIONr_angle_other_deg0.9533.0006745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555.000427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31123.274168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60615.000531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.25915.00029
X-RAY DIFFRACTIONr_chiral_restr0.0930.200489
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0203773
X-RAY DIFFRACTIONr_gen_planes_other0.0020.020744
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6001.8741583
X-RAY DIFFRACTIONr_mcbond_other1.6001.8721582
X-RAY DIFFRACTIONr_mcangle_it2.6412.7961989
X-RAY DIFFRACTIONr_mcangle_other2.6412.7981990
X-RAY DIFFRACTIONr_scbond_it1.8771.9851720
X-RAY DIFFRACTIONr_scbond_other1.8761.9851720
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9072.9152520
X-RAY DIFFRACTIONr_long_range_B_refined4.68321.6193679
X-RAY DIFFRACTIONr_long_range_B_other4.68421.6043676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS shellHighest resolution: 1.391 Å / R factor R free: 0.264 / R factor R work: 0.225 / Lowest resolution: 1.427 Å / Number reflection R free: 374 / Number reflection R work: 6049 / Total number of bins used: 20 / Percent reflection obs: 99.77

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